Supported Data Types

• Expression data
• Affymetrix 3'-IVT arrays
• Affymetrix genechip ST 1.0 arrays
• Agilent single and dual channel arrays
• Illumina expression arrays
• GenePix data
• mAdb Archive data
• GDS datasets from NCBI/GEO
• Other data types through general importer
• RNA Sequencing data
• RNA-seq FASTQ file (Pre-Process through BRB-SeqTools)
• RNA-Seq count data processed through Galaxy web tools

Class comparison for differential expression

• Univariate tests with the option of random variance model
• Multivariate permutation tests
• Significance Analysis of Microarrays(SAM)
• Lassoed Principal Components

Class prediction

• Compound covariate predictor; SVM; Bayesian compound covariate; KNN; DLDA; Nearest centroid
• Adaboost
• PAM
• Lasso logistic regression
• Binary tree prediction

Clustering

• Interactive heat map viewer
• Hierarchical clustering
• Non-negative matrix factorization clustering

2-D and 3-D interactive Scatter-plot

• Phenotype average
• Array vs. Array
• View a demo

Gene Set Enrichment Analysis with many gene sets

• BioCarta
• KEGG
• CGAP
• Broad Institute - MSigDB
• Gene Ontology
• Protein domain
• Transcription factor targets
• MicroRNA targets
• User defined gene lists

Visualization of Samples

• 3-D interactive plot

Survival Analysis

• Survival gene sets analysis
• Survival risk prediction analysis

KEGG Pathway Graphic Tool

The “Gene color coding for KEGG human disease pathways” utility tool displays a KEGG disease pathway graph with selected genes being color-coded by their expression values or fold changes.